sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | hisat2 2.1.0-4 (ppc64el) Wed, 12 Feb 2020 04:47:58 +0000 | +==============================================================================+ Package: hisat2 Version: 2.1.0-4 Source Version: 2.1.0-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: ppc64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-45190cad-2609-4dcc-9698-4a1770cc5d2b' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-Kc5l3i/resolver-UZCWM8' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-11-0810.20.pdiff [13.6 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-11-1410.51.pdiff [13.1 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-11-2012.23.pdiff [20.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-0210.27.pdiff [18.8 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-11-0810.20.pdiff [5022 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-11-1410.51.pdiff [10.9 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-11-2012.23.pdiff [24.6 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-0210.27.pdiff [85.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-0210.27.pdiff [18.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-0210.27.pdiff [85.9 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main ppc64el Packages [8082 kB] Fetched 8472 kB in 2s (4239 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgcc1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1679 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1 amd64 10-20200211-1 [9048 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1 amd64 10-20200211-1 [134 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0 amd64 10-20200211-1 [314 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-base amd64 10-20200211-1 [195 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6 amd64 10-20200211-1 [491 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libquadmath0 amd64 10-20200211-1 [145 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0 amd64 10-20200211-1 [142 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1 amd64 10-20200211-1 [25.7 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1 amd64 10-20200211-1 [99.1 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1 amd64 10-20200211-1 [41.5 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1 amd64 1:10-20200211-1 [41.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libcc1-0 amd64 10-20200211-1 [39.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1679 kB in 0s (40.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../libatomic1_10-20200211-1_amd64.deb ... Unpacking libatomic1:amd64 (10-20200211-1) over (10-20200204-1) ... Preparing to unpack .../libubsan1_10-20200211-1_amd64.deb ... Unpacking libubsan1:amd64 (10-20200211-1) over (10-20200204-1) ... Preparing to unpack .../libtsan0_10-20200211-1_amd64.deb ... Unpacking libtsan0:amd64 (10-20200211-1) over (10-20200204-1) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../libquadmath0_10-20200211-1_amd64.deb ... Unpacking libquadmath0:amd64 (10-20200211-1) over (10-20200204-1) ... Preparing to unpack .../liblsan0_10-20200211-1_amd64.deb ... Unpacking liblsan0:amd64 (10-20200211-1) over (10-20200204-1) ... Preparing to unpack .../libitm1_10-20200211-1_amd64.deb ... Unpacking libitm1:amd64 (10-20200211-1) over (10-20200204-1) ... 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Unpacking libgcc1 (1:10-20200211-1) over (1:10-20200204-1) ... Setting up libgcc1 (1:10-20200211-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../libcc1-0_10-20200211-1_amd64.deb ... Unpacking libcc1-0:amd64 (10-20200211-1) over (10-20200204-1) ... Setting up libgomp1:amd64 (10-20200211-1) ... Setting up libquadmath0:amd64 (10-20200211-1) ... Setting up libatomic1:amd64 (10-20200211-1) ... Setting up libubsan1:amd64 (10-20200211-1) ... Setting up libcc1-0:amd64 (10-20200211-1) ... Setting up liblsan0:amd64 (10-20200211-1) ... Setting up libitm1:amd64 (10-20200211-1) ... Setting up libtsan0:amd64 (10-20200211-1) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2827 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (dsc) [2105 B] Get:2 http://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (tar) [2742 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (diff) [83.0 kB] Fetched 2827 kB in 3s (858 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-Kc5l3i/hisat2-2.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-Kc5l3i' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el Filtered Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [434 B] Get:5 copy:/<>/apt_archive ./ Packages [515 B] Fetched 1906 B in 0s (96.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdmainutils build-essential cpp-9-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-10-base:ppc64el gcc-10-cross-base gcc-9-base:ppc64el gcc-9-cross-base gcc-9-powerpc64le-linux-gnu gcc-9-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:ppc64el libasan5-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libbsd0 libc6:ppc64el libc6-dev libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:ppc64el libgcc-9-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libglib2.0-0 libgomp1:ppc64el libgomp1-ppc64el-cross libicu63 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libstdc++-9-dev libstdc++-9-dev:ppc64el libstdc++-9-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtool libtsan0:ppc64el libtsan0-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-powerpc64le-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:ppc64el libc-l10n:ppc64el locales:ppc64el glibc-doc manpages-dev:ppc64el libstdc++-9-doc libstdc++-9-doc:ppc64el libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax node-katex libmail-box-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx libidn2-0:ppc64el libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdmainutils build-essential cpp-9-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-10-base:ppc64el gcc-10-cross-base gcc-9-base:ppc64el gcc-9-cross-base gcc-9-powerpc64le-linux-gnu gcc-9-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:ppc64el libasan5-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libbsd0 libc6:ppc64el libc6-dev libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:ppc64el libgcc-9-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libglib2.0-0 libgomp1:ppc64el libgomp1-ppc64el-cross libicu63 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libstdc++-9-dev libstdc++-9-dev:ppc64el libstdc++-9-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtool libtsan0:ppc64el libtsan0-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sbuild-build-depends-main-dummy:ppc64el sensible-utils ucf 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After this operation, 517 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-minimal amd64 3.7.6-1+b1 [591 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7-minimal amd64 3.7.6-1+b1 [1813 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 mime-support all 3.64 [37.8 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-2 [661 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-stdlib amd64 3.7.6-1+b1 [1735 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7 amd64 3.7.6-1+b1 [351 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main ppc64el gcc-10-base ppc64el 10-20200211-1 [195 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main ppc64el gcc-9-base ppc64el 9.2.1-28 [195 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-powerpc64le-linux-gnu amd64 2.34-2 [2253 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.10-10 [104 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-10 [2638 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-28 [1697 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-28 [10.7 MB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-powerpc64le-linux-gnu-base amd64 9.2.1-21cross1 [195 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-powerpc64le-linux-gnu amd64 9.2.1-21cross1 [6740 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-powerpc64le-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-21cross1 [190 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200211-1cross1 [191 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-ppc64el-cross all 2.29-9cross1 [1527 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-ppc64el-cross all 10-20200211-1cross1 [30.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-ppc64el-cross all 10-20200211-1cross1 [105 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-ppc64el-cross all 10-20200211-1cross1 [28.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-ppc64el-cross all 10-20200211-1cross1 [9608 B] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-ppc64el-cross all 9.2.1-21cross1 [401 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-ppc64el-cross all 10-20200211-1cross1 [155 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-ppc64el-cross all 10-20200211-1cross1 [318 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-ppc64el-cross all 10-20200211-1cross1 [505 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-ppc64el-cross all 10-20200211-1cross1 [147 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libquadmath0-ppc64el-cross all 10-20200211-1cross1 [152 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-ppc64el-cross all 9.2.1-21cross1 [1262 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-powerpc64le-linux-gnu amd64 9.2.1-21cross1 [7109 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-powerpc64le-linux-gnu amd64 4:9.2.1-3.1 [1480 B] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-ppc64el-cross all 5.4.8-1cross1 [1139 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-ppc64el-cross all 2.29-9cross1 [2657 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-ppc64el-cross all 9.2.1-21cross1 [1728 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-powerpc64le-linux-gnu amd64 9.2.1-21cross1 [7328 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 g++-powerpc64le-linux-gnu amd64 4:9.2.1-3.1 [1188 B] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-8 [710 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-ppc64el all 12.8 [6652 B] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-12 [547 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.47.12 [180 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main ppc64el libgcc-s1 ppc64el 10-20200211-1 [30.5 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main ppc64el libcrypt1 ppc64el 1:4.4.10-10 [96.9 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main ppc64el libc6 ppc64el 2.29-10 [2806 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main ppc64el libasan5 ppc64el 9.2.1-28 [408 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main ppc64el libatomic1 ppc64el 10-20200211-1 [9748 B] Get:106 http://debian.oregonstate.edu/debian unstable/main ppc64el linux-libc-dev ppc64el 5.4.13-1 [1052 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main ppc64el libcrypt-dev ppc64el 1:4.4.10-10 [121 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main ppc64el libc6-dev ppc64el 2.29-10 [2665 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main ppc64el libgomp1 ppc64el 10-20200211-1 [107 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main ppc64el libitm1 ppc64el 10-20200211-1 [28.8 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main ppc64el liblsan0 ppc64el 10-20200211-1 [156 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main ppc64el libtsan0 ppc64el 10-20200211-1 [325 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main ppc64el libstdc++6 ppc64el 10-20200211-1 [546 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main ppc64el libubsan1 ppc64el 10-20200211-1 [148 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main ppc64el libquadmath0 ppc64el 10-20200211-1 [152 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main ppc64el libgcc-9-dev ppc64el 9.2.1-28 [1263 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main ppc64el libstdc++-9-dev ppc64el 9.2.1-28 [1747 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main amd64 pandoc-data all 2.5-3 [349 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main amd64 pandoc amd64 2.5-3+b1 [15.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 105 MB in 1s (80.8 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... 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Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.7-minimal (3.7.6-1+b1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13713 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.5-3_amd64.deb ... Unpacking python3-minimal (3.7.5-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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Selecting previously unselected package libgomp1-ppc64el-cross. Preparing to unpack .../30-libgomp1-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libgomp1-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libitm1-ppc64el-cross. Preparing to unpack .../31-libitm1-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libitm1-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libatomic1-ppc64el-cross. Preparing to unpack .../32-libatomic1-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libatomic1-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libasan5-ppc64el-cross. Preparing to unpack .../33-libasan5-ppc64el-cross_9.2.1-21cross1_all.deb ... Unpacking libasan5-ppc64el-cross (9.2.1-21cross1) ... Selecting previously unselected package liblsan0-ppc64el-cross. Preparing to unpack .../34-liblsan0-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking liblsan0-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libtsan0-ppc64el-cross. Preparing to unpack .../35-libtsan0-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libtsan0-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libstdc++6-ppc64el-cross. Preparing to unpack .../36-libstdc++6-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libstdc++6-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libubsan1-ppc64el-cross. Preparing to unpack .../37-libubsan1-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libubsan1-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libquadmath0-ppc64el-cross. Preparing to unpack .../38-libquadmath0-ppc64el-cross_10-20200211-1cross1_all.deb ... Unpacking libquadmath0-ppc64el-cross (10-20200211-1cross1) ... Selecting previously unselected package libgcc-9-dev-ppc64el-cross. 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Setting up libc6-ppc64el-cross (2.29-9cross1) ... Setting up libdebhelper-perl (12.9) ... Setting up libsqlite3-0:amd64 (3.31.1-2) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:ppc64el (5.4.13-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up gcc-9-powerpc64le-linux-gnu-base:amd64 (9.2.1-21cross1) ... Setting up libyaml-perl (1.30-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cpp-9-powerpc64le-linux-gnu (9.2.1-21cross1) ... Setting up gcc-10-base:ppc64el (10-20200211-1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.2.1-21cross1) ... Setting up gcc-10-cross-base (10-20200211-1cross1) ... Setting up libitm1-ppc64el-cross (10-20200211-1cross1) ... Setting up libatomic1-ppc64el-cross (10-20200211-1cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.10-10) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up linux-libc-dev-ppc64el-cross (5.4.8-1cross1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.29-10) ... Setting up libgcc-s1-ppc64el-cross (10-20200211-1cross1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up binutils-powerpc64le-linux-gnu (2.34-2) ... Setting up pandoc-data (2.5-3) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up cpp-powerpc64le-linux-gnu (4:9.2.1-3.1) ... Setting up gcc-9-base:ppc64el (9.2.1-28) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libstdc++-9-dev:amd64 (9.2.1-28) ... Setting up libc6-dev-ppc64el-cross (2.29-9cross1) ... Setting up libtool (2.4.6-12) ... Setting up libquadmath0-ppc64el-cross (10-20200211-1cross1) ... Setting up libasan5-ppc64el-cross (9.2.1-21cross1) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up m4 (1.4.18-4) ... Setting up libgomp1-ppc64el-cross (10-20200211-1cross1) ... Setting up liblsan0-ppc64el-cross (10-20200211-1cross1) ... Setting up help2man (1.47.12) ... Setting up libtsan0-ppc64el-cross (10-20200211-1cross1) ... Setting up pandoc (2.5-3+b1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.2.1-28) ... Setting up libstdc++6-ppc64el-cross (10-20200211-1cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up build-essential (12.8) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.7-stdlib:amd64 (3.7.6-1+b1) ... Setting up gettext (0.19.8.1-10) ... Setting up libubsan1-ppc64el-cross (10-20200211-1cross1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-9-dev-ppc64el-cross (9.2.1-21cross1) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3.7 (3.7.6-1+b1) ... Setting up gcc-9-powerpc64le-linux-gnu (9.2.1-21cross1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.5-3) ... Setting up libstdc++-9-dev-ppc64el-cross (9.2.1-21cross1) ... Setting up gcc-powerpc64le-linux-gnu (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-9-powerpc64le-linux-gnu (9.2.1-21cross1) ... Setting up g++-powerpc64le-linux-gnu (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-ppc64el (12.8) ... Setting up libcrypt1:ppc64el (1:4.4.10-10) ... Setting up libgcc-s1:ppc64el (10-20200211-1) ... Setting up libc6:ppc64el (2.29-10) ... Setting up libcrypt-dev:ppc64el (1:4.4.10-10) ... Setting up libc6-dev:ppc64el (2.29-10) ... Setting up libstdc++6:ppc64el (10-20200211-1) ... Setting up liblsan0:ppc64el (10-20200211-1) ... Setting up libitm1:ppc64el (10-20200211-1) ... Setting up libtsan0:ppc64el (10-20200211-1) ... Setting up libgomp1:ppc64el (10-20200211-1) ... Setting up dh-autoreconf (19) ... Setting up libasan5:ppc64el (9.2.1-28) ... Setting up libquadmath0:ppc64el (10-20200211-1) ... Setting up libatomic1:ppc64el (10-20200211-1) ... Setting up libubsan1:ppc64el (10-20200211-1) ... Setting up debhelper (12.9) ... Setting up libgcc-9-dev:ppc64el (9.2.1-28) ... Setting up libstdc++-9-dev:ppc64el (9.2.1-28) ... Setting up sbuild-build-depends-main-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.34-2 dpkg-dev_1.19.7 g++-9_9.2.1-28 gcc-8_8.3.0-28 gcc-9_9.2.1-28 libc6-dev_2.29-10 libstdc++-9-dev_9.2.1-28 libstdc++-9-dev-ppc64el-cross_9.2.1-21cross1 libstdc++6_10-20200211-1 libstdc++6-ppc64el-cross_10-20200211-1cross1 linux-libc-dev_5.4.13-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-2 binutils-common_2.34-2 binutils-powerpc64le-linux-gnu_2.34-2 binutils-x86-64-linux-gnu_2.34-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-28 cpp-9_9.2.1-28 cpp-9-powerpc64le-linux-gnu_9.2.1-21cross1 cpp-powerpc64le-linux-gnu_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-ppc64el_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-28 g++-9-powerpc64le-linux-gnu_9.2.1-21cross1 g++-powerpc64le-linux-gnu_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200211-1 gcc-10-cross-base_10-20200211-1cross1 gcc-8_8.3.0-28 gcc-8-base_8.3.0-28 gcc-9_9.2.1-28 gcc-9-base_9.2.1-28 gcc-9-cross-base_9.2.1-21cross1 gcc-9-powerpc64le-linux-gnu_9.2.1-21cross1 gcc-9-powerpc64le-linux-gnu-base_9.2.1-21cross1 gcc-powerpc64le-linux-gnu_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 help2man_1.47.12 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-28 libasan5-ppc64el-cross_9.2.1-21cross1 libatomic1_10-20200211-1 libatomic1-ppc64el-cross_10-20200211-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-2 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-dev_2.29-10 libc6-dev-ppc64el-cross_2.29-9cross1 libc6-ppc64el-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200211-1 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 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perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 readline-common_8.0-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1.2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.1.0-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/hisat2 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git Testsuite: autopkgtest Testsuite-Triggers: bcftools, samtools Build-Depends: debhelper-compat (= 12), help2man , pandoc , python3:any Package-List: hisat2 deb science optional arch=any python3-hisat2 deb python optional arch=all Checksums-Sha1: e428c92bcaf732dd5a0ebab18d2bef6a3bb034dd 2741828 hisat2_2.1.0.orig.tar.xz 64403cf2f599016de6c90b2967dd887cfe713ded 82992 hisat2_2.1.0-4.debian.tar.xz Checksums-Sha256: 8e12e932bb64346eb5ae9c4392146622f30e15b7d043efaecdebd0daea60e143 2741828 hisat2_2.1.0.orig.tar.xz 70bafae685fc9da1cb39b4de0722b34459e95257f4d9dc3c4ed28d8e693c99cb 82992 hisat2_2.1.0-4.debian.tar.xz Files: c3ac50c4c5cf6621b31c18cbfedc70e3 2741828 hisat2_2.1.0.orig.tar.xz 6a78514d4a437024b7fb6aa3d19269bc 82992 hisat2_2.1.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl5C4yMACgkQPCZ2P2xn 5uKjKw/8CD8pEyLyqrhE2koPub+5F6uuOxYkx2mBjBIBQPgBNQo/fF84/25Ue9aN jqKC3wpMiD5d+RXyaTWQBJ/MV3DoFW7/UwiWnPP06Bmn0IKplSvovc8FpohkdrTj l7K1NQ0uRk7PrFgjMzvPW98k7rzHNDIQw+0fG3j8qSjdi2+B/qrhOm1v69gZ+TIc JHeu/59OIytIu6NVvdIxR4RBoctS8Zg/FZhPZrJTIrfvgx7ml4m/eXdRvoIfdt4O Ir+YKHczRitobZL579trLPjb4FkJeKcbmRS9LjHMt1FIm8lIUQSsZ+mYeCq9yl8C dcHanLWHNPefPQ9P+reiitmelKEc4s66k6w0+4Qi7AYmuUervD1PBVF2UpDQHaSc 025SZQH5bQgjC9L8ch74wZIPd7DDkAjCCYZ9E+4oOK7Vfy6slAsLF0ZHfq90bte1 N59rMygIdvcH2ihU5EzXDy1bI5uzwPse4rhdgQ/mTglMfSYPJtBGBrmmXJrMjL5P l4bGq4ikSt3fOLPDXH+0azj0X65MyRCEcMUEW6Bm8AsfA0vFj3n2VZlzBv2a4fFy spI8N4a+FMTPqTtk5oKsfhkmmdSzndvkP/85pyYTqmTSjXsVpgrPGhkXszO8/sbl eucogeKNjZsQVWp+4vn5ra1Vqr+9WVprl/aLLXEzECCKQ9mbpRU= =G74b -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 11 17:23:47 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.1.0-4.dsc dpkg-source: info: extracting hisat2 in /<> dpkg-source: info: unpacking hisat2_2.1.0.orig.tar.xz dpkg-source: info: unpacking hisat2_2.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.ppc64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-45190cad-2609-4dcc-9698-4a1770cc5d2b SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -appc64el -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-architecture: warning: specified GNU system type powerpc64le-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="11 February 2020" all doc make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=11 February 2020" all doc make[2]: Entering directory '/<>' powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’: hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2125:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2125 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:642:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 642 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { spliced_aligner.h:1298:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1298 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:936:25: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:5792:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5792 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:327:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 327 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/bits/locale_conv.h:41, from /usr/powerpc64le-linux-gnu/include/c++/9/locale:43, from /usr/powerpc64le-linux-gnu/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/powerpc64le-linux-gnu/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ make[2]: Nothing to be done for 'doc'. make[2]: Leaving directory '/<>' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man: can't get `--help' info from ./hisat2 Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:33: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:28: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-12T04:57:32Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 75708 Build-Time: 532 Distribution: unstable Fail-Stage: build Foreign Architectures: ppc64el Host Architecture: ppc64el Install-Time: 25 Job: hisat2_2.1.0-4 Machine Architecture: amd64 Package: hisat2 Package-Time: 574 Source-Version: 2.1.0-4 Space: 75708 Status: attempted Version: 2.1.0-4 -------------------------------------------------------------------------------- Finished at 2020-02-12T04:57:32Z Build needed 00:09:34, 75708k disk space